No matter how much a Malevolent Phantom knew, the only thing that was ultimately recovered from them was the extent of humanity's mastery over the soul—nothing else.

According to Donna, when a Malevolent Phantom was killed, only a tiny fragment of their remaining soul was retrieved. It was not enough to record everything they had learned—only the most critical information was preserved.

So, in the end, whatever intelligence a Malevolent Phantom gathered during its time on Earth did not matter.